% Matlab script to reproduce the figures in the paper:
%
%   Tom Michoel and Yves van de Peer, "A helicoidal transfer matrix model
%      for inhomogeneous DNA melting", Phys. Rev. E 73, 011908 (2006)
%      arXiv:q-bio/0507036
%
% Warning: it takes some time to do all these computations!

%%%% DNA sequences %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% pBR322 sequence
pbr322 = [4 4 2 4 2 1 4 3 4 4  4 3 1 2 1 3 2 4 4 1  4 2 1 4 2 3 1 4 1 1 ...
          3 2 4 4 4 1 1 4 3 2  3 3 4 1 3 4 4 4 1 4 2 1 2 1 3 4 4 1 1 1  4 ...
          4 3 2 4 1 1 2 3 2  1 3 4 2 1 3 3 2 1 2  2 3 4 3 4 1 4 3 1 1  1 ...
          4 2 4 1 1 2 1 1 4 3 2 3 2 4 2 1 4 2 3  4 2 1 4 2 2 4 2 3 3  2 1 ...
          2 2 3 4 2 1 2 2  2 4 3 3 1 4 3 2 4 3  4 1 3 3 2 1 4 1 3 3 2 4 4 ...
          3 3 4 4 1 4 3  2 2 3 3 4 1 2 4 3 2  2 3 3 3 2 2 4 2 4 4  3 2 3 ...
          3 3 1 4 1 4 2  3 4 2 2 1 4 4 2 2 3 1 2 1 3 2 1 4 2 3 2  2 1 3 4 ...
          2 1 2 4 1 4 3 3 2 3 4 3 2 4 3 2  4 1 3 2 3 2 4 1 4 1  4 3 2 3 4 ...
          4 3 1 4 3 2 1 1 4 4 4 2 4 1 4  3 2 3 2 1 2 2 2 3 4  4 2 4 2 3 3 ...
          1 3 2 1  2 4 3 4 2 2 3 1 2 2  3 2 4 4 4 3 3 2 2 3 2 2 3 2 2 2 1 ...
          3 4 2  2 4 3 2 4 2 3 2 4 4  2 3 2 4 1 2 4 4 3 3  1 3 2 2 1 2 4 ...
          1 4 2  3 1 2 4 1 2 3 2 3 1 4 2 1 4 3 3 2 3 1 2  2 1 2 1 2 2 2 3 ...
          4 2  2 4 3 4 3 3 1 4 2 2  4 2 4 1 2 3 2 2 3 3  1 2 3 2 1 4 2 3 ...
          4 3 3 2 2 3 3 2 1 4 2 1 2 2 3 3 2 3 2 2 1 2  1 3 3 4 3 2 3 3 4 ...
          4  3 2 4 3 3 2 3 2 2 4  1 4 1 4 2 3 2 2 3 1 2 1 4 2 1 2 2 3 1 4 ...
          3 3 3 3 1 1 3 1 4 2  3 3 3 2 4 2 3 2 2 1  2 4 4 2 3 3 3 2 4 2 ...
          1 4 3 1 3 2 3 2 4 4 3 4 4 4 2 3 3 2 3 4  3 3 3 4 1 4 3 3 4 3  3 ...
          2 1 3 3 2 2 2 2 3  4 3 3 2 2 3 3 3 3 3  1 2 4 3 4 4 3 3 3 2 3 2 ...
          2 1 4 2 4 2 2 4  4 3 2 1 4 3 2 1 2 2  1 4 4 2 2 4 4 3 2 3  3 2 ...
          3 3 2 3 3 4 3 2  4 2 1 1 2 3 3 2 2 4 2 1 1 2 2 4 1 2 4 1  2 4 3 ...
          3 3 2 4 3 2 4  4 2 2 4 1 1 4 3 2 1 3 3 1 3 4 2 3 2 1 4  1 1 3 3 ...
          3 1 3 1 3 2 3 4 2 3 1 2 2 3 1 4  3 2 2 2 4 4 3 1 3 1  3 2 2 4 4 ...
          2 1 1 2 2  2 1 3 4 2 1 3 2 4 2  2 4 4 2 2 3 3 4 3 3 3 2 3 2 3 3 ...
          3 3 2 1  4 3 1 2 4 1 4 2 3 4  2 3 2 2 3 2 1 2 4 4  1 4 3 1 2 4 ...
          3 4 2 4  4 2 4 4 4 1 4 2 1 4 3 2 1 1 2 4 2 3 4 1  3 3 1 2 1 3 3 ...
          4 3 2  2 3 3 2 1 3 2 3 2 4  2 4 3 3 3 4 2 1 4 4  4 4 2 3 3 2 3 ...
          1 3 3 1 2 2 3 2 4 4 4 2 3  2 4 3 3 1 3 2 3 2 3 1 2 3 1 4 3 1 4 ...
          2 3  3 2 2 4 3 4 2 3 2 4  4 3 2 3 3 4 1 4 4 2 3 3 1 1 4 2 4 4 3 ...
          2  1 2 3 2 2 2 4 2 3 2  4 2 1 1 3 2 2 4 4 2  3 4 2 1 2 4 3 3 4 ...
          2 2 2 3 2 2 1 2 2 1 1 1 2 3 4 4 4 2 3 3 2  3 1 3 1 1 3 2 1 3 3 ...
          2 2 1 4 4 1 4 2 3 2  2 3 3 2 1 4 3 3 2 3  3 2 2 3 1 2 3 2 3 2 4 ...
          3 3 3 2 4 1 2 3 4  2 4 4 3 2 4 3 3 2 3  4 4 2 3 2 3 1 2 3 2  3 ...
          1 3 3 2 4 3 3 1 4  3 3 2 2 4 4 2 2 2 2 1 4 4 1 4 3 1 4 4 2 4 4 ...
          2 4 2 3 2 4 4 2  2 3 3 2 3 3 2 1 4 2  3 3 3 1 4 3 2 2 2 3  2 3 ...
          4 4 3 2 1 3 3 2 2 1 4 3 2 4 3 4 2 2  1 3 3 2 1 3 3 4 1 3  1 4 3 ...
          1 2 3 1 2 2 1  4 2 1 3 3 3 1 2 1 3  2 4 4 2 1 1 3 3 1 4 2 3 2 4 ...
          2 3 2 3 3 2  4 2 4 4 1 2 2 1 3 2  2 4 1 1 2 4 4 2 3 1  4 2 1 2 ...
          4 3 3 1 2 2 3 2 4 3 1 4 2 3 4 2 1 2 3 3 2 3 1 4 4 4  1 4 3 2 2 ...
          3 2 2 4 2  3 3 2 3 1 3 2 1 2 1  4 3 3 1 1 2 3 3 3 4  4 3 3 2 1 ...
          4 3 3 1 4 4 3 4 1 3 3 2 3 2 2  3 2 2 2 4 1 4 1 2 2  4 4 3 4 2 4 ...
          3 2 2 4 2 2 2 2 3 2 3 4 4 3  2 3 4 2 3 2 3 3 4 3 2 1 4 3 3 1 3 ...
          2 2 3  3 3 2 2 1 2 2 4 2 3  1 2 2 4 3 1 1 4 3 3  1 1 3 2 2 3 3 ...
          2 3 3  2 1 2 2 4 2 3 2 4 1 1 2 3 3 1 4 4 2 1 2  2 1 2 4 2 2 1 1 ...
          3 1  1 4 4 3 3 1 3 2 2 1  1 4 2 1 1 4 4 2 4 4  3 2 3 3 1 3 1 1 ...
          2 4 3 4 3 1 1 4 3 2 3 2  1 1 1 2 2 1 1 2 2 2  4 4 3 3 2 1 3 1 1 ...
          2  1 4 1 4 2 2 1 4 2 3 2 3 4 2 2 3 2 2 1 4 2 4 2 2 1 3 2 1 3 2 ...
          2 3 2 1 2 3 2 3 3 2 3 2 1 4 2 4 2 3 3 3  2 1 3 2 3 4 4 3 3 3  4 ...
          2 2 4 3 3 2 2 1 2 3 3 3 4 3 2 3 2 1 4  3 1 4 2 3 4 3 2 4 2  2 4 ...
          3 4 2 3 4 4 3 1  3 3 1 2 2 2 3 3 2 4  1 3 3 2 4 3 3 2 3 3 3 3 4 ...
          4 3 2 2 4 4 1  2 4 3 3 4 4 1 3 2 1  3 1 1 4 3 1 1 4 2 1 2 2 3 1 ...
          4 1 2 3 2 3  1 3 2 3 1 1 2 3 4 3 1 1 3 2 3 1 2 4 3 2  4 3 2 4 3 ...
          2 1 1 1 1  2 3 4 2 4 3 2 3 1 2  2 4 3 1 3 2 1 1 2 1  1 2 1 4 3 ...
          1 1 4 3 3 4 2 4 4 2 3 3 4 4 4 2 2 3 4 3 4 4 4 2 3  4 1 1 1 3 4 ...
          2 4 3 3  1 1 1 2 3 2 3 3 1 1 3 4 2 1 3 2 3 2 2 2 4 3 2 1 2 2 1 ...
          4 4 1  4 3 4 4 2 2 3 3 1 4  2 4 3 2 1 4 2 3 2 1  3 3 1 4 3 2 4 ...
          3 2 4  3 3 2 4 1 2 2 2 4 3 4 3 3 1 1 2 1 2 2 4  1 2 1 4 2 4 3 4 ...
          1 4  4 1 1 2 3 1 1 3 2 3  2 4 3 3 2 1 4 4 3 1  2 2 2 4 3 1 3 4 ...
          3 1 4 4 4 4 4 2 4 2 4 3  3 4 2 2 2 3 2 2 3 2  1 4 2 2 1 4 1 2 2 ...
          3 2 2 1 3 4 4 3 4 4 4  1 2 2 2 4 2 1 2 1 1 2 3 4 4 2 2 1 3 4 1 ...
          1 2 2 3 3 3 2 1 4 3  4 4 2 1 4 2 1 4 2 1 3 4 1 1 2 2 2 3 4 1  4 ...
          2 3 4 3 1 3 2 1 4 2 2 4 2 4 2 4 2 3 4  4 4 2 1 4 2 3 3 4 1  4 2 ...
          1 4 4 1 2 2 2 2  2 1 4 3 1 1 2 1 3 1 1 1 4 4 2 2 2 2 2 4 4 1 2 ...
          1 2 3 3 1 3 3  2 1 4 2 1 1 3 4 3 1 2 2 1 1 1 2 1 3 3 1  1 1 1 1 ...
          1 2 2 3 2 2  2 4 4 1 1 2 1 4 3 3 2 2 2 3 2 4 4 4 1 4  2 1 3 1 1 ...
          3 2 2 1 3  1 2 1 4 4 1 1 2 3 2  4 4 2 4 3 3 1 3 1 1  1 2 4 2 1 ...
          1 2 3 1 3 2 4 3 3 1 2 3 2 3 3  1 4 3 1 1 2 1 3 3 2 1 3 1 2 1 4 ...
          2 4 3 4  3 1 1 4 2 3 2 4 4 2  1 2 3 1 2 2 1 2 3 2 4 3 1 4 3 1 3 ...
          2 4 4 4 1 2 2 3 2 1 3 2 4  3 2 2 4 2 3 2 3 2 3  4 4 4 2 3 3 4 3 ...
          1 4  3 1 2 3 3 4 3 1 1 1 1 2 2 4 2 4 3 1 2 1  2 1 4 3 2 1 3 2 4 ...
          2  2 2 3 3 1 3 1 2 3 3  4 2 1 2 1 3 2 4 4 3 4 2 4 3 4 1 1 3 2 3 ...
          3 1 4 3 2 2 3 3 3 1  3 2 1 3 1 2 1 1 3 2  2 2 3 4 2 1 3 3 3 2 ...
          3 2 3 4 2 1 3 2 3 3  3 4 3 4 4 3 3 2 3 3 3 4 3 4 2 3 3 3 3 2 3 ...
          2 1 3 2 2 1 4 3 1  2 2 2 1 3 4 2 1 2 3  4 1 3 2 3 1 4 1 3 2  3 ...
          3 1 3 4 3 4 1 4 1 2 4 3 3 2 4 4 1 1 2  4 1 4 3 2 3 3 2 1 4  2 1 ...
          3 1 3 2 1 3 1 4  4 3 4 1 2 4 3 1 3 1  3 4 3 2 1 2 2 1 4 1 4 3 2 ...
          3 3 4 3 4 3 1  1 1 4 1 2 2 3 2 1 2  1 3 1 4 3 2 3 4 1 1  3 3 1 ...
          3 1 1 1 1 4 1  2 2 3 2 1 4 2 1 3 3 2 3 2 4 2 4 4 2 2 3  2 4 4 2 ...
          2 4 2 3 2 4  2 1 2 4 3 1 2 4 2 3  2 4 3 2 3 2 4 2 3 3 4 2 3 4 4 ...
          2 3 3 2 4 3 2 3 3 2 3 1 3 2 3  3 4 1 4 2 1 3 2 4 2  1 2 4 2 1 1 ...
          1 3 3 2 3 3 4 1 1 4 1 2 3 3  4 4 1 4 2 2 1 2 1 3 1 1 4 2 1 3 3 ...
          3 3 1  4 1 1 2 3 2 1 3 3 1  1 1 3 1 1 2 1 4 3 4  3 1 3 2 1 1 1 ...
          1 3 3  2 2 1 3 2 1 1 1 1 3 3 2 2 1 3 3 1 1 2 2  3 4 1 1 1 1 1 3 ...
          3 2  2 3 2 3 4 4 3 2 4 3 3 2 3 4 4 4 4 4 2 2  1 4 1 3 3 2 4 2 2 ...
          3 2 2 2 2 2 2 4 3 1 2  3 1 3 2 1 4 2 1 2 1  1 1 1 1 4 2 3 1 2 3 ...
          2 4 2 1 1 3 4 2 1 3 1 3 3 4 3 3 2 3 1 1 1 2 2 2 3 1 2 1 3 3  1 ...
          2 4 1 4 1 1 1 3 1 4 1 2 2 1 3 3 2 3 4  4 4 2 2 2 2 2 4 3 3  1 1 ...
          3 2 4 2 2 2 4 2 3 4 3 2 3 2 4 2 4 2  2 4 3 4 4 2 2 3 1 2  2 2 4 ...
          3 2 2 3 2 4 4  1 2 2 3 3 1 4 1 2 2  4 3 4 2 2 3 2 2 4 4 4 2 4 2 ...
          2 2 4 4 2 3  3 3 1 1 3 2 3 4 3 3  2 3 2 4 4 4 2 4 2 1 4 1 3 2 4 ...
          2 1 2 3 2  4 3 4 1 3 3 4 1 4 2 4 2 1 3 4 4 2 3 3 4  3 4 1 3 3 4 ...
          2 3 4 4  2 3 2 4 2 2 1 1 3 2 4 3 3 3 2 4 3 4 3 4  3 2 1 2 3 1 1 ...
          2 2 2 2 2 2 3 4 4 2 1 3 2 2 2 3 1 2 2 3 2 4 3  2 3 2 2 4 4 1 4 ...
          2 2  3 3 4 1 1 2 4 1 4 2  3 4 2 4 4 3 1 3 4 2 2 1 1 2 2 2 3 3 4 ...
          1  1 3 1 2 1 2 3 1 2 4 4 1 4 2 3 2 2 1 2 4  3 3 2 1 3 2 1 3 2 2 ...
          1 2 4 3 3 4 1 1 2 1 3 3 1 4 4 1 3 2 1 3  1 3 2 3 1 3 3 4 1 4  3 ...
          4 1 3 3 2 3 3 4 3  2 4 1 2 1 3 1 3 4 4  2 4 4 3 1 1 3 4 3 3 4 3 ...
          3 2 2 4 1 1 2 4  1 2 3 3 2 4 1 2 1 2  4 1 3 1 1 3 3 1 2 1 3 4 1 ...
          4 4 4 3 3 4 1  4 2 4 3 2 3 2 4 2 4 3 2 4 3 1 1 3 2 2 1 3 4 4 1 ...
          2 2 4 4 2 3  3 1 1 1 1 1 3 1 3 4 4 3 3 4 1 3 2 4 2 4  4 3 1 4 2 ...
          2 3 3 2 1 1 1 2 1 1 1 2 2 1 2  2 3 2 4 3 3 4 1 3 2  3 3 4 3 3 4 ...
          4 4 4 4  4 4 3 4 4 4 3 2 1 1  3 2 1 3 2 1 3 1 4 4 1 2 3 2 3 2 1 ...
          3 1 1  1 1 1 1 1 3 3 1 4 2  4 2 1 1 3 1 1 3 1 4  2 2 4 4 4 3 1 ...
          4 2 4 4 4 4 2 4 1 2 3 3 3 3 4 2 4 3 1 2 3 2 4  2 1 3 4 3 3 1 1 ...
          2 3  1 1 1 1 2 4 2 1 2 3  4 4 1 1 3 3 3 1 4 4  4 4 3 3 4 2 1 4 ...
          3 1 3 1 4 4 1 4 2 1 1 1  1 1 3 3 1 4 2 4 4 2 1 2 2 4 1 3 1 4 2 ...
          2  4 4 4 4 1 1 1 4 4 1  1 1 1 1 4 3 1 1 3 4 4 4 4 1 1 1 4 2 1 1 ...
          4 2 4 1 1 1 3 4 1 4  1 4 1 4 3 1 3 4 1 1  1 2 4 4 3 3 4 2 4 3 ...
          1 2 1 3 4 4 1 2 2 1 1 4 3 2 4 4 1 1 4 2  1 3 4 3 1 3 3 2 1 2  2 ...
          4 1 4 2 4 2 1 3 2  3 1 4 2 4 3 4 2 4 1  4 4 4 2 3 4 4 2 1 4 2 2 ...
          1 4 1 3 4 4 3 2  2 4 3 1 2 4 2 2 2 2  3 4 2 3 4 3 4 1 3 1  4 1 ...
          1 2 4 1 2 3 1 4 1 2 3 3 3 1 3 3 3 2 4 4 1 2 2 1 4 2 4 3 3 2 2 2 ...
          2 1 3 4 3 2  4 3 2 1 1 4 3 1 4 1  2 2 3 2 3 1 3 1 2 2  2 1 2 3 ...
          2 4 2 1 2 2 3 3 2 4 2 2 1 3 1 4  4 4 1 4 2 1 3 2 1 1  4 1 1 1 2 ...
          2 1 3 2 2 1 3 2 2 3 3 1 1 3 3  3 2 2 3 1 3 2 3 2 1 3 1 1 3 4 3 ...
          3 4 2 2  4 3 2 1 1 2 4 4 4 1  4 2 2 3 2 2 4 2 2 1 4 2 2 1 3 4 2 ...
          4 1 4 4 1 1 4 4 3 4 4 3 2 2 3 3 3 1 1 3 2 4 1  3 1 3 4 1 1 3 4 ...
          1 3  4 4 2 3 2 2 1 3 4 4  1 1 4 1 3 4 4 4 3 2  3 2 1 1 2 3 4 4 ...
          3 4 4 3 2 2 1 4 4 3 2 4  3 2 1 3 3 2 1 4 2 3  4 3 3 4 3 4 2 1 2 ...
          3 2 4 2 3 4 2 3 4 4 4  3 3 4 1 4 3 3 2 4 4 2 1 4 4 2 1 3 2 4 2 ...
          2 3 3 4 4 2 2 2 1 1  2 3 1 4 2 1 1 3 3 2  3 1 3 4 4 1 2 1 4 3 ...
          1 4 2 2 2 2 2 1 4 3 4 4 3 4 3 2 1 1 1 1  1 1 3 2 3 3 4 4 1 3  2 ...
          4 2 2 4 4 2 3 3 4 2 2 4 2 2 3 1 4 2 3  4 4 3 4 2 1 3 1 1 3 4 1 ...
          1 3 4 4 3 3 2 2  3 2 1 3 4 3 4 4 1 4  2 1 2 4 2 1 4 3 3 4 4 1 4 ...
          3 3 2 1 3 2 1  2 4 3 2 1 4 1 1 4 4 2 4 2 4 4 1 2 4 3 4  2 1 4 3 ...
          2 2 1 4 2 2 3 4 1 1 3 1 4 3 2 4  4 4 4 2 4 3 4 3 1 2  4 3 3 4 3 ...
          1 3 4 1 2 4 2 1 1 2 2 1 1 3 4  2 1 4 4 2 4 3 1 3 1 1 4 1 3 4 3 ...
          4 1 4 3  2 3 3 2 3 1 2 2 3 1  3 4 4 3 2 4 2 4 4 3 2 2 2 3 3 2 3 ...
          4 2 1  1 2 1 2 3 3 3 1 4 1  1 4 1 2 2 3 2 3 2 2 1 2 1 4 1 3 2 1 ...
          3 1  1 2 4 4 4 1 1 1 1 3 4 3 2 4 2 1 4 2 1 4  4 3 3 1 1 1 1 2 3 ...
          4  4 2 4 4 2 3 3 3 3 2  3 1 1 1 1 2 4 2 4 2  1 1 3 3 1 4 2 4 4 ...
          1 2 2 3 2 4 3 4 4 3 1 3 1 4 2 2 1 3 4 4 2  3 1 4 3 4 1 1 2 2 2 ...
          1 2 4 2 3 4 3 2 1 2  2 2 1 1 2 4 3 1 4 2 4 4 2 1 3 2 1 4 2 4  4 ...
          4 4 1 2 4 4 4 2 1  2 2 1 3 2 3 4 4 4 2  4 3 3 3 4 3 1 3 2 1  1 ...
          1 1 1 2 1 3 3 1 1 3 3 2 1 1 1 1 4 3 2  2 3 2 1 1 1 1 1 1 3 3 3 ...
          1 1 4 1 1 3 3 3  2 3 1 2 1 2 3 3 1 1  1 4 3 4 4 3 1 1 4 1 2 4 2 ...
          1 4 1 2 4 2 4  4 2 2 4 4 4 4 4 2 1  1 4 1 4 4 1 4 4 3 1 1 3 2 1 ...
          4 4 4 1 4 2  1 3 3 3 4 4 1 4 4 3 4 2 4 2 1 4 3 1 3 2  3 3 1 4 1 ...
          2 1 4 1 4  4 4 3 1 1 4 3 4 1 4 4 4 1 3 1 1 1 1 1 4  1 1 1 2 1 1 ...
          1 4 1 3 3 3 3 4 4 2 2 3 2 3 2 1 2 1 4 4 4 2 2 2  2 3 1 1 1 1 3 ...
          4 3 2  2 1 2 2 4 3 1 2 3 4  2 4 1 1 3 1 1 1 2 2 1 4 4 1 4 4 1 4 ...
          2 1  4 3 1 2 1 4 4 1 1 2  2 4 1 4 1 1 1 1 1 4  1 3 3 2 3 4 1 4 ...
          2 1  2 3 1 3 3 2 2 2 4 4 4 2 3 4 2 4 4 2 1 1  3 1 1 ];

% inserted AT-rich fragment
s1 = [1 1 3 4 4 3 1 1 2 1 1 1 1 4];
ins = zeros(1,245);
for k=1:17
  ins((k-1)*14+1:k*14) = s1;
end
ins(239:245) = [1 1 3 4 4 3 1];

% PN/MCS13 sequence
pnmcs13 = [pbr322(1:971) ins pbr322(972:4363)];

% C-MYC sequence
cmyc=[1 3 2 4 4 3 4 4 4 3 3 2 2 3 4 4 4 4 1 3 3 3 4 4 4 3 4 4 3 3 1 1 4 4 ...
      4 4 4 4 4 4 4 2 3 4 2 4 1 4 3 4 1 2 4 4 3 4 3 1 1 4 4 1 4 4 4 2 1 2 ...
      3 4 4 4 3 2 2 1 4 4 1 2 2 3 3 4 4 2 4 2 2 1 4 1 3 3 3 4 3 1 4 3 4 4 ...
      2 1 4 4 1 3 2 1 3 4 3 3 4 3 1 4 1 3 3 4 4 1 1 4 4 4 4 2 1 2 2 1 4 2 ...
      4 2 4 4 1 4 3 2 3 3 4 4 3 1 1 4 1 3 4 2 1 2 2 4 2 4 3 1 1 2 2 1 2 4 ...
      4 4 4 4 2 2 4 2 2 1 3 4 1 1 2 4 2 2 4 2 4 4 4 2 4 4 2 3 3 1 2 2 4 4 ...
      2 4 3 2 1 3 2 2 1 1 2 2 4 3 1 1 1 3 1 1 4 1 1 2 1 1 3 3 1 3 3 4 3 3 ...
      2 4 3 3 1 1 1 2 4 4 3 4 4 4 4 1 1 3 3 1 1 2 2 3 2 2 4 3 4 2 2 4 4 2 ...
      2 2 2 2 3 2 4 3 3 1 1 1 2 2 4 4 3 2 1 2 2 4 2 3 3 1 2 3 2 4 2 2 4 3 ...
      2 4 2 2 4 3 2 2 2 2 2 1 2 2 4 3 1 2 2 2 2 2 3 2 2 2 4 2 3 4 4 3 1 2 ...
      1 4 2 2 1 3 3 2 3 2 3 1 4 3 1 4 2 4 2 4 3 2 4 3 2 2 1 3 4 1 3 1 3 3 ...
      3 2 1 2 1 2 4 4 1 2 4 4 4 1 2 4 4 4 2 3 2 1 1 1 2 2 4 3 1 1 2 3 2 3 ...
      3 3 4 3 2 4 3 2 2 2 1 3 1 3 1 3 3 3 3 3 2 3 3 1 3 3 3 1 1 1 3 1 2 3 ...
      2 4 4 4 3 2 1 3 2 1 1 1 1 4 2 2 1 3 2 1 4 1 3 2 3 1 4 4 3 3 4 4 3 2 ...
      4 2 2 2 2 3 2 3 4 4 4 3 2 3 3 2 1 1 1 3 3 2 2 4 3 3 1 3 3 2 1 3 3 1 ...
      3 4 1 1 4 4 4 3 2 1 1 4 2 2 4 4 1 1 1 3 2 4 3 1 1 4 4 3 4 3 2 1 3 4 ...
      3 2 1 4 2 3 3 1 4 4 4 3 3 1 1 3 2 4 1 2 4 1 4 1 4 4 2 1 2 4 4 1 1 2 ...
      1 2 4 4 3 1 1 2 3 2 4 3 1 3 2 4 3 2 1 1 1 2 4 2 1 1 2 3 3 3 4 1 1 4 ...
      1 1 2 2 2 1 4 2 4 4 3 1 1 2 1 3 2 3 4 1 2 1 4 3 2 4 1 4 1 2 1 2 1 2 ...
      1 2 2 2 2 4 4 4 2 2 2 2 2 3 1 1 4 4 3 4 4 4 4 2 4 2 4 4 4 4 3 3 1 3 ...
      3 4 3 3 4 3 3 1 3 3 3 1 3 1 3 1 1 1 1 3 4 4 4 1 2 4 4 1 1 1 1 4 3 2 ...
      2 4 4 4 3 3 3 4 3 1 3 3 3 1 2 2 1 1 3 3 1 4 3 1 3 1 1 3 1 1 4 3 4 4 ...
      4 4 4 4 3 4 4 4 4 4 2 1 4 3 2 2 3 4 3 3 1 1 4 1 1 2 1 2 1 1 1 1 4 1 ...
      1 1 1 1 1 4 2 2 2 3 1 3 3 3 1 1 4 1 4 1 2 1 4 4 1 4 1 4 1 4 4 1 1 1 ...
      4 1 4 1 3 1 4 2 1 4 4 4 2 1 3 3 3 1 3 2 1 1 1 2 1 1 1 4 2 1 4 3 4 3 ...
      4 3 3 3 3 2 4 3 3 3 2 1 1 2 4 1 3 2 4 3 1 3 4 2 3 1 1 3 2 3 4 1 1 1 ...
      4 1 1 1 1 4 3 4 3 1 1 4 1 2 1 2 3 4 4 4 3 2 3 3 3 4 4 1 2 1 4 1 2 1 ...
      3 4 3 2 1 2 4 4 4 2 1 2 4 1 3 4 1 4 4 2 1 3 1 1 1 1 1 1 4 4 3 4 3 1 ...
      3 4 2 1 3 4 3 1 1 2 4 1 3 3 1 1 1 4 4 1 1 4 3 2 2 4 3 3 1 1 3 3 2 1 ...
      3 2 2 1 1 1 4 4 4 4 1 1 4 4 1 3 2 4 2 1 1 3 1 2 4 2 2 2 2 2 2 2 2 2 ...
      2 2 2 2 1 1 1 1 1 1 1 3 3 2 1 2 3 3 1 1 3 4 1 1 4 1 2 4 2 2 4 2 4 2 ...
      2 4 2 4 4 2 4 4 4 3 1 4 2 1 3 1 1 4 2 3 1 4 3 2 1 4 4 4 4 4 4 3 4 3 ...
      2 1 4 3 1 2 2 3 2 1 4 4 4 2 2 1 1 4 1 1 4 1 1 1 1 3 3 3 3 1 1 1 3 1 ...
      3 3 1 2 2 4 3 3 1 1 1 3 3 1 1 4 4 1 1 1 2 3 4 2 2 3 3 4 4 4 3 4 2 2 ...
      3 3 3 3 1 3 3 1 1 1 3 1 3 4 4 1 1 2 3 3 4 4 4 4 4 4 4 2 1 2 1 1 3 3 ...
      3 4 2 4 2 4 3 2 4 3 1 2 4 2 2 2 2 2 3 3 2 4 2 3 3 4 2 2 1 2 1 1 3 2 ...
      4 2 4 2 2 1 2 4 4 3 2 2 2 2 4 4 4 4 1 3 3 1 1 3 4 2 2 3 3 4 2 2 2 3 ...
      2 3 3 4 4 2 3 3 3 4 1 2 2 2 2 2 4 3 2 2 2 2 4 2 2 2 1 4 1 4 4 2 4 2 ...
      2 2 3 4 2 4 1 3 2 1 2 2 4 4 4 3 1 4 4 4 2 4 2 2 2 1 1 1 2 2 2 3 3 2 ...
      1 3 2 2 2 3 1 3 1 2 4 3 4 4 3 2 1 1 1 2 2 3 3 2 3 2 2 1 2 1 3 3 3 2 ...
      3 2 1 1 1 3 3 3 3 1 4 4 4 3 4 2 4 2 4 4 2 4 3 1 1 1 2 2 4 3 3 2 4 3 ...
      1 3 1 1 1 4 4 3 3 3 1 1 2 4 2 2 3 4 3 4 3 3 3 1 3 3 2 3 4 3 3 3 3 3 ...
      4 3 3 3 1 2 3 3 4 3 3 3 3 4 1 2 1 3 1 2 4 3 3 2 1 3 1 3 1 3 2 1 3 3 ...
      2 1 1 2 2 4 2 2 2 4 2 4 2 3 2 2 2 4 1 3 2 2 2 1 3 2 4 2 4 3 3 1 1 2 ...
      1 3 3 2 1 3 1 2 1 2 1 4 2 4 2 1 3 3 3 2 4 1 1 1 2 1 3 1 2 3 2 2 4 2 ...
      2 2 3 2 1 2 3 3 3 3 2 2 2 2 1 2 3 3 1 1 3 2 2 4 3 1 3 2 1 3 3 2 3 3 ...
      3 3 2 1 3 3 1 3 3 3 3 2 3 3 4 1 4 2 4 3 2 4 3 2 4 4 4 3 3 2 1 3 2 1 ...
      1 1 4 4 3 3 3 3 3 1 2 4 2 1 3 4 2 4 3 3 3 4 3 3 1 1 3 3 4 1 4 2 2 1 ...
      1 4 2 2 1 3 1 4 1 3 2 4 3 4 3 2 1 4 1 2 1 4 1 1 4 3 2 1 4 1 1 4 1 2 ...
      1 4 3 1 2 4 2 2 2 2 2 2 1 1 2 1 1 1 4 3 2 1 1 4 3 3 3 1 3 4 4 4 1 4 ...
      4 2 1 4 1 1 2 3 2 3 2 4 2 4 2 2 1 1 3 4 1 4 1 2 3 4 3 3 2 1 1 4 3 2 ...
      3 4 4 3 2 4 3 3 3 4 4 1 4 4 4 4 1 1 4 2 1 4 4 2 4 1 3 3 2 1 4 2 3 4 ...
      4 4 4 2 2 4 2 2 4 4 1 4 3 2 2 4 2 4 1 4 2 1 4 4 2 2 4 2 2 2 4 1 4 2 ...
      4 1 2 1 2 4 1 1 2 1 4 2 2 2 1 2 3 2 4 2 4 3 1 1 2 3 2 3 2 3 2 2 2 1 ...
      4 4 1 1 4 1 2 2 2 4 4 2 4 4 4 2 2 4 2 2 1 2 4 2 4 2 2 2 4 3 3 3 1 2 ...
      4 2 4 4 3 1 4 2 1 1 1 3 2 3 2 3 3 2 2 2 4 4 4 2 2 2 2 1 3 2 2 4 4 1 ...
      3 2 3 1 3 3 2 3 2 2 2 4 3 2 1 3 2 2 4 3 3 4 1 2 3 2 3 2 3 4 3 3 2 3 ...
      4 3 3 2 3 3 4 3 3 3 2 3 2 3 2 1 3 4 3 2 3 4 4 2 4 2 4 3 4 3 4 3 3 1 ...
      3 3 3 2 1 3 2 4 3 4 4 2 2 3 2 2 4 3 2 3 1 4 3 1 4 4 4 1 4 1 2 4 2 1 ...
      2 1 3 3 1 2 1 1 3 3 1 4 3 2 3 3 4 4 4 3 4 2 1 1 1 2 1 3 4 1 2 4 3 2 ...
      4 1 2 3 3 1 3 3 1 3 2 1 3 2 1 3 1 3 1 1 1 3 3 3 1 3 1 3 3 3 4 4 4 3 ...
      1 3 1 3 3 3 1 3 2 1 1 1 1 3 1 1 1 1 4 3 3 4 1 3 3 2 3 2 3 2 3 4 1 3 ...
      4 4 1 1 4 4 2 1 4 3 2 3 3 2 4 2 4 2 4 4 1 2 4 2 4 3 4 4 4 1 2 1 4 2 ...
      2 4 1 3 1 3 2 4 1 3 1 3 4 3 2 4 2 3 3 2 4 3 2 2 2 3 3 2 4 3 1 3 4 2 ...
      4 2 2 4 2 2 2 2 1 2 2 4 4 2 2 2 2 1 2 2 2 4 2 2 2 2 1 2 2 2 4 2 2 2 ...
      2 1 4 1 1 3 2 3 2 2 2 2 4 2 2 2 3 3 3 4 4 2 2 2 1 1 1 3 2 1 3 1 3 3 ...
      3 2 3 4 3 3 3 3 3 1 1 1 1 3 1 1 1 1 1 1 3 1 4 2 2 4 2 4 2 4 2 3 2 4 ...
      1 1 4 2 4 2 2 3 2 2 2 1 2 2 3 3 2 2 2 4 4 4 1 4 1 1 4 3 2 3 1 3 3 3 ...
      4 2 4 3 3 1 2 3 3 2 4 3 1 3 3 1 2 2 2 2 2 3 1 3 2 4 3 4 3 2 4 3 2 4 ...
      2 3 2 3 3 2 2 3 2 2 1 2 2 3 2 2 3 3 3 2 2 2 2 3 3 2 2 3 4 2 2 2 4 3 ...
      3 2 4 2 2 2 2 4 2 2 4 3 2 2 4 2 3 1 3 1 1 3 3 3 2 1 3 3 3 2 4 4 2 4 ...
      2 1 3 1 3 3 2 4 4 3 3 2 3 3 3 1 1 1 1 1 3 1 1 2 3 3 1 3 3 3 1 3 3 3 ...
      1 4 2 3 2 3 2 4 3 1 3 4 1 4 1 1 1 1 3 2 2 3 3 4 4 4 4 2 3 3 3 3 2 4 ...
      4 4 1 4 2 4 1 1 2 4 2 3 2 4 3 4 1 3 4 1 1 4 4 2 2 1 3 2 3 1 3 1 3 3 ...
      2 1 3 1 3 3 3 1 3 2 3 1 3 2 3 3 3 2 3 3 2 2 3 3 2 4 1 3 3 3 4 3 3 1 ...
      1 3 1 3 2 2 3 3 3 2 3 1 3 2 1 3 1 3 2 4 3 2 3 2 4 3 2 3 3 3 2 3 4 2 ...
      2 4 3 3 3 1 1 3 3 3 1 3 1 4 2 2 3 3 1 3 2 3 1 1 4 1 3 3 3 3 3 2 4 4 ...
      2 3 2 2 4 2 4 3 3 2 2 2 1 3 2 2 2 4 2 2 2 3 2 4 3 1 4 2 2 2 2 2 1 3 ...
      2 2 1 3 2 3 3 4 2 2 3 2 1 1 2 2 2 4 4 3 2 2 3 2 1 4 2 2 1 2 3 1 1 1 ...
      2 4 4 4 3 2 2 2 1 4 1 3 2 1 3 2 3 3 3 2 3 3 3 2 1 2 4 4 4 3 2 1 2 4 ...
      3 3 1 1 2 4 4 1 2 1 1 2 1 2 2 2 3 1 3 2 1 1 3 3 1 2 3 2 3 1 2 4 2 4 ...
      2 2 2 3 1 2 3 2 3 3 3 3 1 3 3 2 4 1 4 4 2 4 3 2 2 2 1 4 4 4 3 3 3 3 ...
      1 2 1 2 4 4 2 2 2 2 3 2 2 3 2 4 3 2 2 1 3 3 1 2 2 2 3 2 4 4 2 4 2 4 ...
      3 1 1 1 3 3 2 4 2 4 2 2 4 4 3 2 1 3 2 4 3 2 4 4 1 3 1 2 3 2 4 3 3 1 ...
      4 4 4 4 4 4 4 2 3 3 3 4 1 3 4 3 3 1 1 1 1 2 2 1 3 3 4 1 1 3 2 1 2 2 ...
      3 1 1 3 4 2 2 1 2 4 4 3 2 2 4 4 4 4 1 1 4 4 4 1 4 4 4 4 4 4 4 1 4 2 ...
      1 2 4 4 4 1 1 4 3 2 4 3 1 3 1 4 3 1 3 4 2 3 1 1 4 3 2 2 4 1 1 1 4 1 ...
      3 3 3 4 3 4 2 4 4 4 4 2 4 2 2 2 1 4 4 2 2 4 3 2 3 2 4 1 4 4 3 1 2 1 ...
      2 4 4 4 4 2 4 2 1 3 1 3 4 1 3 4 4 1 4 3 3 4 1 1 2 4 3 3 3 3 2 4 3 3 ...
      3 3 4 3 3 3 3 3 3 4 1 1 4 2 2 1 3 1 1 2 4 3 3 1 4 2 3 3 3 3 4 1 1 1 ...
      3 4 3 1 2 4 4 3 4 2 1 1 3 1 4 3 3 3 1 3 1 3 3 1 3 1 1 3 3 2 1 3 1 3 ...
      3 3 1 1 1 1 2 3 3 3 1 1 4 3 3 4 4 4 4 4 1 1 3 1 2 4 1 2 2 2 4 4 4 2 ...
      3 1 3 1 4 4 4 2 4 3 2 2 4 4 1 4 3 1 1 4 1 4 1 4 4 2 1 2 3 2 4 3 1 2 ...
      4 2 2 2 3 3 2 2 3 3 4 2 3 3 1 2 1 4 4 2 2 4 3 2 4 4 4 1 4 4 3 4 3 4 ...
      4 1 1 4];
% modified C-MYC sequence
cmycmod = [cmyc(1:780), cmyc(825:end)];
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% start by setting the model parameters
DNA_melt_preferences;

figure(1)
% PN/MCS13: Opening probability at T=310 and Gamma=-0.042 with free b.c.
temp = 310;
Gamma = -0.042;
bc = 'free';
prob = melt_prob(temp,Gamma,pnmcs13,bc);
plot(prob)
grid on;
axis([0 length(pnmcs13) 0 1]);
xlabel('Sequence position');
ylabel('Opening probability');

figure(2)
% PN/MCS13: Correlation function C^n_m for n=3489 (top) and n=2200
% (bottom) at T=310 and Gamma=-0.042 with free b.c.
% NOTE: this figure is slightly different than the paper figure, it plots
% <h(r_n-12) h(r_m-12)> - <h(r_n-12)><h(r_m-12)>
% i.e. correlation between opening events at n and m.
temp = 310;
Gamma = -0.042;
bc = 'free';
n = 3489;
[prob1,cor1] = melt_cor(n,temp,Gamma,pnmcs13,'free');
subplot(2,1,1)
plot(n-200:n+200,cor1(n-200:n+200));
axis tight;
grid on;
n = 2200;
[prob2,cor2] = melt_cor(n,temp,Gamma,pnmcs13,'free');
subplot(2,1,2)
plot(n-200:n+200,cor2(n-200:n+200));
axis tight;
grid on;

figure(3)
% PN/MCS13: Differential melting curve and melting map (shaded area)
% (temperature increment 0.5, Gamma=-0.042) with free b.c.
tempI = 295;
tempF = 340;
step = 0.5;
Gamma = -0.042;
bc = 'free';
[temp,gamma,diff,tempr] = melt_curve(tempI,tempF,step,Gamma,pnmcs13,bc);
[AX,H1,H2] = plotyy(temp,diff,tempr,0:length(pnmcs13),'plot','filltr');
xlabel('Temperature (K)');
set(get(AX(1),'Ylabel'),'String','d\gamma /dT');
set(get(AX(2),'Ylabel'),'String','Sequence position (kbp)');
axis(AX(1),'tight');
axis(AX(2), [tempI, tempF, 0, length(pnmcs13)]);
seqticks = 0:1000:length(pnmcs13);
set(AX(2),'YTick',seqticks);
set(AX(2),'YTickLabel',0:1:length(seqticks)-1);
set(AX(1),'XGrid','on')
alpha(H2,0.3);

figure(4)
% PN/MCS13: Differential melting curve and melting map (shaded area) with
% homogeneous stacking and twist energy (K=0.1486, E=0.0942, theta0=0.60755)
% (temperature increment 0.5, Gamma=-0.042) with free b.c.
p = getpref('DNA_melt');
K = (sum(sum(p.K))/16)*ones(4);
E = (sum(sum(p.E))/16)*ones(4);
theta0 = (sum(sum(p.theta0))/16)*ones(4);
l0 = sqrt(p.h^2*ones(4) + 4*p.r0^2*(sin(0.5*theta0)).^2); 
setpref('DNA_melt',{'K','E','theta0','l0'},{K,E,theta0,l0});
tempI = 305;
tempF = 350;
step = 0.5;
Gamma = -0.042;
bc = 'free';
[temp,gamma,diff,tempr] = melt_curve(tempI,tempF,step,Gamma,pnmcs13,bc);
[AX,H1,H2] = plotyy(temp,diff,tempr,0:length(pnmcs13),'plot','filltr');
xlabel('Temperature (K)');
set(get(AX(1),'Ylabel'),'String','d\gamma /dT');
set(get(AX(2),'Ylabel'),'String','Sequence position (kbp)');
axis(AX(1),'tight');
axis(AX(2), [tempI, tempF, 0, length(pnmcs13)]);
seqticks = 0:1000:length(pnmcs13);
set(AX(2),'YTick',seqticks);
set(AX(2),'YTickLabel',0:1:length(seqticks)-1);
set(AX(1),'XGrid','on');
alpha(H2,0.3);
DNA_melt_preferences;

figure(5)
% PN/MCS13: Differential melting curve and melting map (shaded area) with
% homogeneous stacking and twist energy (K=0.1486, E=0.0942, theta0=0.60755)
% (temperature increment 0.5, Gamma=-0.042) with free b.c.
p = getpref('DNA_melt');
K = 0.65*ones(4);
E = 0.04*ones(4);
theta0 = 0.60707*ones(4);
l0 = sqrt(p.h^2*ones(4) + 4*p.r0^2*(sin(0.5*theta0)).^2); 
setpref('DNA_melt',{'K','E','theta0','l0'},{K,E,theta0,l0});
tempI = 310;
tempF = 340;
step = 0.5;
Gamma = -0.042;
bc = 'free';
[temp,gamma,diff,tempr] = melt_curve(tempI,tempF,step,Gamma,pnmcs13,bc);
[AX,H1,H2] = plotyy(temp,diff,tempr,0:length(pnmcs13),'plot','filltr');
xlabel('Temperature (K)');
set(get(AX(1),'Ylabel'),'String','d\gamma /dT');
set(get(AX(2),'Ylabel'),'String','Sequence position (kbp)');
axis(AX(1),'tight');
axis(AX(2), [tempI, tempF, 0, length(pnmcs13)]);
seqticks = 0:1000:length(pnmcs13);
set(AX(2),'YTick',seqticks);
set(AX(2),'YTickLabel',0:1:length(seqticks)-1);
set(AX(1),'XGrid','on');
alpha(H2,0.3);
DNA_melt_preferences;

figure(6)
% PN/MCS13: Differential melting curves for Gamma=-0.05, 0.0, 0.05 (left
% to right, temperature increment 0.5) with free b.c.
Gamma = -0.05;
tempI = 280;
tempF = 340;
step = 0.5;
bc = 'free';
[temp1,gamma1,diff1,tempr1] = melt_curve(tempI,tempF,step,Gamma,pnmcs13,bc);
Gamma = 0.0;
tempI = 340;
tempF = 410;
step = 0.5;
bc = 'free';
[temp2,gamma2,diff2,tempr2] = melt_curve(tempI,tempF,step,Gamma,pnmcs13,bc);
Gamma = 0.05;
tempI = 410;
tempF = 480;
step = 0.5;
bc = 'free';
[temp3,gamma3,diff3,tempr3] = melt_curve(tempI,tempF,step,Gamma,pnmcs13,bc);

plot(temp1,diff1);
hold on;
plot(temp2,diff2);
plot(temp3,diff3);
hold off;
grid on;
xlabel('Temperature (K)');
ylabel('d\gamma /dT');


figure(7)
% C-MYC: F_{tq}(Gamma)+alpha*Gamma for alpha=0.572, 0.581, 0.590, 0.600
% (sigma=-0.06, -0.045, -0.03, -0.015) at T=310 with closed b.c.
temp = 310;
Lk0 = sum(p.theta0(cmyc(1:end-1)+4*(cmyc(2:end)-1)));
Gamma = (-0.1:0.001:0.0);
f=zeros(length(Gamma),4);
l=1;
for sigma = [ -0.06, -0.045, -0.03, -0.015]
  alpha = (1+sigma)*Lk0/length(cmyc)
  for k=1:length(Gamma)
    f(k,l) = free_energy(temp,Gamma(k),cmyc,'closed') + alpha*Gamma(k);
  end
  l = l+1;
end
plot(Gamma,f);
grid on;
xlabel('\Gamma (eV/rad)');
ylabel('F_{tq}(\Gamma) + \alpha \Gamma');

figure(8)
% C-MYC: Absolute value of u(omega) at sigma=-0.03 and T=310
% (omega-interval 5x10^(-4)) with closed b.c.
temp = 310;
sigma = -0.03;
bc = 'closed';
seq=cmyc;
Gamma = (-0.1:0.001:0.0);
omega = (-0.04:0.0005:0.04)';
[prob,u,un] = melt_prob_lk(temp,sigma,cmyc,bc,Gamma,omega);
plot(omega,abs(u));
grid on;
xlabel('\omega');
ylabel('|u(\omega)|');

figure(9)
% C-MYC: Real value of u(omega) at sigma=-0.03 and T=310
% (omega-interval 5x10^(-4)) with closed b.c.
plot(omega,real(u));
grid on;
xlabel('\omega');
ylabel('Re u(\omega)');

figure(10)
% Opening probability at T=310 and fixed superhelical density sigma=-0.03
% for the C-MYC sequence (top) and the modified C-MYC sequence (bottom)
[prob2,u2,un2] = melt_prob_lk(temp,sigma,cmycmod,bc,Gamma,omega);
subplot(2,1,1)
plot(prob);
axis([0 length(cmyc) 0 1]);
grid on;
xlabel('Sequence position');
ylabel('Opening probability');
subplot(2,1,2)
plot(prob2);
axis([0 length(cmyc) 0 1]);
grid on;
xlabel('Sequence position');
ylabel('Opening probability');

figure(11)
% Opening probability at T=310 in fixed torque ensemble for the C-MYC
% sequence (Gamma=-0.041475, <sigma>=-0.03004) (top) and the modified
% C-MYC sequence (Gamma=-0.044365, <sigma>=-0.03003) (bottom)
bc = 'closed';
Gamma = -0.041475;
prob3 = melt_prob(temp,Gamma,cmyc,bc);
Gamma = -0.044365
prob4 = melt_prob(temp,Gamma,cmycmod,bc);
subplot(2,1,1)
plot(prob3);
axis([0 length(cmyc) 0 1]);
grid on;
xlabel('Sequence position');
ylabel('Opening probability');
subplot(2,1,2)
plot(prob4);
axis([0 length(cmyc) 0 1]);
grid on;
xlabel('Sequence position');
ylabel('Opening probability');
